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(-) Description

Title :  N-DOMAIN OF GRP94 LACKING THE CHARGED DOMAIN IN COMPLEX WITH RADICICOL
 
Authors :  D. T. Gewirth, R. M. Immormino
Date :  14 Jul 04  (Deposition) - 05 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Grp94, Hsp90, Bergerat, Chaperone, Endoplasmic Reticulum, Radicicol (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. T. Gewirth, R. M. Immormino
N-Domain Of Grp94 Lacking The Charged Domain In Complex With Radicicol
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDOPLASMIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX-NB-GRP94(69-337DELTA41)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN OF GRP94 RESIDUES (69-337)
    Gene: TRA1
    Organism Common: DOG
    Organism Scientific: CANIS LUPUS FAMILIARIS
    Organism Taxid: 9615
    Strain: FAMILIARIS
    Synonym: 94 KDA GLUCOSE-REGULATED PROTEIN, GRP94

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2PG49Ligand/IonTETRAETHYLENE GLYCOL
3RDC2Ligand/IonRADICICOL
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2PG44Ligand/IonTETRAETHYLENE GLYCOL
3RDC1Ligand/IonRADICICOL
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2PG45Ligand/IonTETRAETHYLENE GLYCOL
3RDC1Ligand/IonRADICICOL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:104 , ASN A:107 , ASP A:110 , ALA A:111 , LYS A:114 , ASP A:149 , MET A:154 , ASN A:162 , LEU A:163 , PHE A:199 , THR A:245 , ILE A:247 , PG4 A:403 , HOH A:413 , HOH A:415 , HOH A:458 , HOH A:532BINDING SITE FOR RESIDUE RDC A 301
02AC2SOFTWARETHR A:212 , ARG A:237 , THR A:240 , THR A:248 , PG4 A:402 , HOH A:488 , HOH A:509 , HOH A:511 , HOH A:538BINDING SITE FOR RESIDUE PG4 A 401
03AC3SOFTWARELYS A:137 , THR A:148 , THR A:246 , TRP A:282 , PG4 A:401 , HOH A:516BINDING SITE FOR RESIDUE PG4 A 402
04AC4SOFTWAREASP A:110 , ASP A:113 , LYS A:114 , LEU A:117 , RDC A:301 , HOH A:507BINDING SITE FOR RESIDUE PG4 A 403
05AC5SOFTWARELYS A:75 , PHE A:76 , ALA A:77 , HOH A:455BINDING SITE FOR RESIDUE PG4 A 404
06AC6SOFTWARELEU B:104 , ASN B:107 , ASP B:110 , ALA B:111 , LYS B:114 , ASP B:149 , MET B:154 , ASN B:162 , LEU B:163 , PHE B:199 , THR B:245 , ILE B:247 , PG4 B:410 , HOH B:413 , HOH B:423 , HOH B:529BINDING SITE FOR RESIDUE RDC B 302
07AC7SOFTWAREILE B:210 , THR B:212 , ARG B:237 , THR B:248 , HOH B:456 , HOH B:487BINDING SITE FOR RESIDUE PG4 B 405
08AC8SOFTWARELYS B:137 , THR B:148 , TRP B:282 , TRP B:333 , HOH B:501BINDING SITE FOR RESIDUE PG4 B 406
09AC9SOFTWAREASN B:129 , ASN B:239 , GLY B:242 , HOH B:530BINDING SITE FOR RESIDUE PG4 B 407
10BC1SOFTWAREASP B:262 , THR B:263 , ASN B:266 , HOH B:507 , HOH B:527 , HOH B:545BINDING SITE FOR RESIDUE PG4 B 408
11BC2SOFTWAREASN A:83 , LYS A:87 , ILE A:90 , SER A:227 , HOH A:479 , ASN B:83 , MET B:86 , LYS B:87 , ILE B:90 , SER B:227BINDING SITE FOR RESIDUE 1PE A 409
12BC3SOFTWARELYS B:114 , RDC B:302 , HOH B:537 , HOH B:548BINDING SITE FOR RESIDUE PG4 B 410

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U0Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U0Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U0Z)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HSP90PS00298 Heat shock hsp90 proteins family signature.ENPL_CANLF94-103
 		  2A:94-103
B:94-103
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HSP90PS00298 Heat shock hsp90 proteins family signature.ENPL_CANLF94-103
 		  1A:94-103
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HSP90PS00298 Heat shock hsp90 proteins family signature.ENPL_CANLF94-103
 		  1-
B:94-103

(-) Exons   (0, 0)

(no "Exon" information available for 1U0Z)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:211
 aligned with ENPL_CANLF | P41148 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:264
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333    
           ENPL_CANLF    74 EKFAFQAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKMTEAQEDGQSTSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKTVWDWELMN 337
               SCOP domains d1u0za_ A: HSP90                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1u0zA00 A:74-337  [code=3.30.565.10, no name defined]                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...........eeeeee....eeeeee.....hhhhhhhhhhh.---hhhhhhhhhhh-------hhhhhhhhhhhhhhhhh.eeeeeeeee......eeeee....eeeee.........eeeeeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeeee.-------------------------------------------..eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------HSP90     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1u0z A  74 EKFAFQAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTI---GTSEFLNKMTE-------TSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSK-------------------------------------------TVWDWELMN 337
                                    83        93       103       113       123       133       143       153       163  |   |173      |  -    |  193       203       213       223       233       243       253       263       273       283 |       -         -         -         -     | 333    
                                                                                                                      166 170       180     188                                                                                              285                                         329        


Chain B from PDB  Type:PROTEIN  Length:226
 aligned with ENPL_CANLF | P41148 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:297
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       
           ENPL_CANLF    41 GSRTDDEVVQREEEAIQLDGLNASQIRELREKSEKFAFQAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKMTEAQEDGQSTSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKTVWDWELMN 337
               SCOP domains d1                        u0zb_ B: HSP90                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1u                        0zB00 B:65-337  [code=3.30.565.10, no name defined]                                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .h------------------------hhhhhh..ee..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...........eeeeee....eeeeee.....hhhhhhhhhhh....hhhhhhhhhhhhh-----hhhhhhhhhhhhhhhhh.eeeeeeeee......eeeee....eeeee.........eeeeeeee.hhhhhhhhhhhhhhhhhhhh......eeeeeee.------------------------------------------.eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------HSP90     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u0z B  65 GS------------------------HMLREKSEKFAFQAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKMTEAQ-----TSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSKT------------------------------------------TVWDWELMN 337
                             |       -         -      | 70        80        90       100       110       120       130       140       150       160       170       180 |     190       200       210       220       230       240       250       260       270       280     |   -         -         -         -       330       
                            66                       67                                                                                                                182   188                                                                                               286                                        329
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1U0Z)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ENPL_CANLF | P41148)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
biological process
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0006950    response to stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    GO:0030433    ubiquitin-dependent ERAD pathway    The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    GO:0016529    sarcoplasmic reticulum    A fine reticular network of membrane-limited elements that pervades the sarcoplasm of a muscle cell; continuous over large portions of the cell and with the nuclear envelope; that part of the endoplasmic reticulum specialized for calcium release, uptake and storage.

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  ENPL_CANLF | P41148
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ENPL_CANLF | P41148: 1qy5 1qy8 1qye 1tbw 1tc0 1tc6 1u0y 1u2o 1ysz 1yt0 1yt1 1yt2 2esa 2exl 2fyp 2gfd 2gqp 2h8m 2hch 2hg1 2o1t 2o1u 2o1v 2o1w 3o2f 5in9

(-) Related Entries Specified in the PDB File

1qy5 CRYSTAL STRUCTURE OF THE N-DOMAIN OF THE ER HSP90 CHAPERONE GRP94 IN COMPLEX WITH THE SPECIFIC LIGAND NECA
1qy8 CRYSTAL STRUCTURE OF THE N-DOMAIN OF THE ER HSP90 CHAPERONE GRP94 IN COMPLEX WITH RADICICOL
1qye CRYSTAL STRUCTURE OF THE N-DOMAIN OF THE ER HSP90 CHAPERONE GRP94 IN COMPLEX WITH 2-CHLORODIDEOXYADENOSINE
1qyh CRYSTAL STRUCTURE OF THE N-DOMAIN OF GRP94 LACKING THE CHARGED DOMAIN IN COMPLEX WITH NECA
1tc0 LIGAND INDUCED CONFORMATIONAL SHIFTS IN THE N-TERMINAL DOMAIN OF GRP94, OPEN CONFORMATION COMPLEXED WITH THE PHYSIOLOGICAL PARTNER ATP
1tc6 LIGAND INDUCED CONFORMATIONAL SHIFT IN THE N-TERMINAL DOMAIN OF GRP94, OPEN CONFORMATION ADP-COMPLEX
1u0y